Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications

Benjamin D. Redelings, Ian Holmes, Gerton Lunter, Tal Pupko, Maria Anisimova

Research output: Contribution to journalReview articlepeer-review

Abstract

Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic rearrangements, adaptation, and speciation. Recent advances in long-read sequencing technologies allow detailed inference of insertions and deletion variation in species and populations. Yet, despite their importance, evolutionary studies have traditionally ignored or mishandled insertions and deletions due to a lack of comprehensive methodologies and statistical models of insertions and deletion dynamics. Here, we discuss methods for describing insertions and deletion variation and modeling insertions and deletions over evolutionary time. We provide practical advice for tackling insertions and deletions in genomic sequences and illustrate our discussion with examples of insertions and deletion-induced effects in human and other natural populations and their contribution to evolutionary processes. We outline promising directions for future developments in statistical methodologies that would allow researchers to analyze insertions and deletion variation and their effects in large genomic data sets and to incorporate insertions and deletions in evolutionary inference.

Original languageEnglish
Article numbermsae177
JournalMolecular Biology and Evolution
Volume41
Issue number9
DOIs
StatePublished - 1 Sep 2024

Keywords

  • alignment
  • deletion
  • evolution
  • indel
  • insertion
  • phylogeny

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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